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This page was generated on 2025-02-03 12:05 -0500 (Mon, 03 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4494
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4400
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1130/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.20.0  (landing page)
Lauren McIver
Snapshot Date: 2025-01-30 13:00 -0500 (Thu, 30 Jan 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_20
git_last_commit: 1cacd4c
git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on nebbiolo2

To the developers/maintainers of the Maaslin2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Maaslin2
Version: 1.20.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.20.0.tar.gz
StartedAt: 2025-01-30 23:32:18 -0500 (Thu, 30 Jan 2025)
EndedAt: 2025-01-30 23:36:18 -0500 (Thu, 30 Jan 2025)
EllapsedTime: 239.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Maaslin2 84.708  0.732  85.418
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.15
Current TMB package version is 1.9.16
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-01-30 23:34:13.070804 INFO::Writing function arguments to log file
2025-01-30 23:34:13.113309 INFO::Verifying options selected are valid
2025-01-30 23:34:13.145651 INFO::Determining format of input files
2025-01-30 23:34:13.147057 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-30 23:34:13.152098 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-30 23:34:13.153327 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-30 23:34:13.155598 INFO::Filter data based on min abundance and min prevalence
2025-01-30 23:34:13.156454 INFO::Total samples in data: 1595
2025-01-30 23:34:13.157262 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-30 23:34:13.160939 INFO::Total filtered features: 0
2025-01-30 23:34:13.161918 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-30 23:34:13.169653 INFO::Total filtered features with variance filtering: 0
2025-01-30 23:34:13.17067 INFO::Filtered feature names from variance filtering:
2025-01-30 23:34:13.171517 INFO::Running selected normalization method: TSS
2025-01-30 23:34:14.270871 INFO::Bypass z-score application to metadata
2025-01-30 23:34:14.272211 INFO::Running selected transform method: AST
2025-01-30 23:34:14.288662 INFO::Running selected analysis method: LM
2025-01-30 23:34:14.794926 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-30 23:34:15.117323 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-30 23:34:15.278123 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-30 23:34:15.419949 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-30 23:34:15.56944 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-30 23:34:15.712885 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-30 23:34:15.859832 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-30 23:34:15.996025 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-30 23:34:16.103906 WARNING::Fitting problem for feature 8 a warning was issued
2025-01-30 23:34:16.255499 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-30 23:34:16.364508 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-30 23:34:16.568932 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-30 23:34:16.715978 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-30 23:34:16.892401 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-30 23:34:17.031686 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-30 23:34:17.163359 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-30 23:34:17.315326 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-30 23:34:17.460698 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-30 23:34:17.60887 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-30 23:34:17.749358 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-30 23:34:17.897435 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-30 23:34:18.04203 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-30 23:34:18.188503 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-30 23:34:18.330375 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-30 23:34:18.479432 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-30 23:34:18.618877 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-30 23:34:18.759048 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-30 23:34:18.904131 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-30 23:34:19.043661 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-30 23:34:19.187747 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-30 23:34:19.339282 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-30 23:34:19.483351 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-30 23:34:19.632745 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-30 23:34:19.774266 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-30 23:34:19.943934 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-30 23:34:20.107972 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-30 23:34:20.259194 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-30 23:34:20.639133 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-30 23:34:20.776257 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-30 23:34:20.91952 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-30 23:34:21.073563 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-30 23:34:21.206233 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-30 23:34:21.342709 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-30 23:34:21.486056 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-30 23:34:21.631775 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-30 23:34:21.777733 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-30 23:34:21.915386 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-30 23:34:22.057654 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-30 23:34:22.19411 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-30 23:34:22.336802 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-30 23:34:22.485962 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-30 23:34:22.62063 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-30 23:34:22.760757 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-30 23:34:22.903277 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-30 23:34:23.036858 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-30 23:34:23.17431 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-30 23:34:23.324544 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-30 23:34:23.455814 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-30 23:34:23.59867 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-30 23:34:23.750735 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-30 23:34:23.880846 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-30 23:34:24.035472 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-30 23:34:24.168801 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-30 23:34:24.302217 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-30 23:34:24.444973 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-30 23:34:24.591176 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-30 23:34:24.776738 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-30 23:34:24.909785 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-30 23:34:25.047693 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-30 23:34:25.206534 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-30 23:34:25.345845 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-30 23:34:25.504476 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-30 23:34:25.648755 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-30 23:34:25.792054 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-30 23:34:25.93061 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-30 23:34:26.063444 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-30 23:34:26.200378 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-30 23:34:26.344174 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-30 23:34:26.485495 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-30 23:34:26.633333 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-30 23:34:26.77884 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-30 23:34:26.924351 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-30 23:34:27.072896 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-30 23:34:27.207632 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-30 23:34:27.34978 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-30 23:34:27.500777 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-30 23:34:27.641714 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-30 23:34:27.787539 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-30 23:34:27.938024 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-30 23:34:28.07466 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-30 23:34:28.256679 INFO::Counting total values for each feature
2025-01-30 23:34:28.286645 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-30 23:34:28.381171 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-30 23:34:28.477397 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-30 23:34:28.583022 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-30 23:34:28.630997 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-30 23:34:28.657773 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-30 23:34:28.66303 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-30 23:34:28.668142 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-01-30 23:34:28.679827 INFO::Writing function arguments to log file
2025-01-30 23:34:28.685146 INFO::Verifying options selected are valid
2025-01-30 23:34:28.686066 INFO::Determining format of input files
2025-01-30 23:34:28.687085 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-30 23:34:28.69156 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-30 23:34:28.6925 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-30 23:34:28.693971 INFO::Filter data based on min abundance and min prevalence
2025-01-30 23:34:28.69477 INFO::Total samples in data: 1595
2025-01-30 23:34:28.695553 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-30 23:34:28.69965 INFO::Total filtered features: 0
2025-01-30 23:34:28.700577 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-30 23:34:28.707555 INFO::Total filtered features with variance filtering: 0
2025-01-30 23:34:28.708578 INFO::Filtered feature names from variance filtering:
2025-01-30 23:34:28.709371 INFO::Running selected normalization method: NONE
2025-01-30 23:34:28.710126 INFO::Bypass z-score application to metadata
2025-01-30 23:34:28.710892 INFO::Running selected transform method: AST
2025-01-30 23:34:28.730553 INFO::Running selected analysis method: LM
2025-01-30 23:34:28.732159 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-30 23:34:28.864577 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-30 23:34:29.011416 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-30 23:34:29.14228 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-30 23:34:29.277923 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-30 23:34:29.42106 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-30 23:34:29.562751 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-30 23:34:29.700829 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-30 23:34:29.83702 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-30 23:34:29.96799 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-30 23:34:30.104939 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-30 23:34:30.224833 WARNING::Fitting problem for feature 11 a warning was issued
2025-01-30 23:34:30.366498 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-30 23:34:30.497327 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-30 23:34:30.639259 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-30 23:34:30.770714 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-30 23:34:30.915501 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-30 23:34:31.020412 WARNING::Fitting problem for feature 16 a warning was issued
2025-01-30 23:34:31.156623 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-30 23:34:31.299769 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-30 23:34:31.434189 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-30 23:34:31.571326 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-30 23:34:31.707147 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-30 23:34:31.843059 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-30 23:34:31.986181 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-30 23:34:32.113043 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-30 23:34:32.263921 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-30 23:34:32.397316 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-30 23:34:32.530737 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-30 23:34:32.674214 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-30 23:34:32.801553 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-30 23:34:32.930246 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-30 23:34:33.070824 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-30 23:34:33.205034 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-30 23:34:33.3471 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-30 23:34:33.495844 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-30 23:34:33.626724 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-30 23:34:33.765805 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-30 23:34:33.898762 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-30 23:34:34.031851 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-30 23:34:34.171743 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-30 23:34:34.298198 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-30 23:34:34.432153 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-30 23:34:34.562813 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-30 23:34:34.696235 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-30 23:34:34.860377 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-30 23:34:35.006245 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-30 23:34:35.159712 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-30 23:34:35.295017 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-30 23:34:35.433218 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-30 23:34:35.565355 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-30 23:34:35.702478 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-30 23:34:35.824145 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-30 23:34:35.965487 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-30 23:34:36.085158 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-30 23:34:36.211554 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-30 23:34:36.3359 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-30 23:34:36.469337 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-30 23:34:36.611256 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-30 23:34:36.737939 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-30 23:34:36.865936 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-30 23:34:37.006824 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-30 23:34:37.130998 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-30 23:34:37.260458 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-30 23:34:37.398284 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-30 23:34:37.532065 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-30 23:34:37.67377 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-30 23:34:37.805181 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-30 23:34:37.947415 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-30 23:34:38.077183 WARNING::Fitting problem for feature 67 a warning was issued
2025-01-30 23:34:38.216636 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-30 23:34:38.351682 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-30 23:34:38.486709 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-30 23:34:38.633093 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-30 23:34:38.762973 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-30 23:34:38.808913 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-30 23:34:38.945902 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-30 23:34:39.077352 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-30 23:34:39.226211 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-30 23:34:39.358447 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-30 23:34:39.511997 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-30 23:34:39.643131 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-30 23:34:39.776475 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-30 23:34:39.925986 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-30 23:34:40.058148 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-30 23:34:40.197191 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-30 23:34:40.337577 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-30 23:34:40.461647 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-30 23:34:40.596417 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-30 23:34:40.724579 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-30 23:34:40.903116 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-30 23:34:41.06687 INFO::Counting total values for each feature
2025-01-30 23:34:41.095079 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-30 23:34:41.188517 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-30 23:34:41.282158 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-30 23:34:41.382582 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-30 23:34:41.446303 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-30 23:34:41.507848 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-30 23:34:41.513164 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-30 23:34:41.517422 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 29.001   0.555  29.546

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin284.708 0.73285.418